ap/ncbi-toolkit: Removed.

ap/ncbi-toolkit/build-fixes.diff

@@ -1,40 +0,0 @@
-diff -Naur ncbi.orig/ncbi/corelib/ncbienv.c ncbi/ncbi/corelib/ncbienv.c
---- ncbi.orig/ncbi/corelib/ncbienv.c	2007-05-04 15:43:59.000000000 +0200
-+++ ncbi/ncbi/corelib/ncbienv.c	2009-03-27 01:37:01.000000000 +0100
-@@ -812,6 +812,8 @@
-     if (fp == NULL) {
-       path[0] = '\0';
-       pth = getenv ("NCBI");
-+      if (pth == NULL)
-+        pth = "/etc/ncbi";
-       if (pth != NULL) {
-         Nlm_FileBuildPath(path, pth, str + 1);
-         fp = Ncbienv_FileOpen (path, "r");
-diff -Naur ncbi.orig/ncbimake/makedis.csh ncbi/ncbi/make/makedis.csh
---- ncbi.orig/ncbi/make/makedis.csh	2008-12-30 16:15:10.000000000 +0100
-+++ ncbi/ncbi/make/makedis.csh	2009-03-27 01:39:23.000000000 +0100
-@@ -342,8 +342,8 @@
- #
- 
- #uncomment two following lines to don't build X11 apps
--#set HAVE_OGL=0
--#set HAVE_MOTIF=0
-+set HAVE_OGL=0
-+set HAVE_MOTIF=0
- 
- # if $OPENGL_TARGETS (in <platform>.ncbi.mk) is defined, 
- # then add the appropriate flags, libraries, and binaries for OpenGL apps
-diff -Naur ncbi/ncbi.orig/platform/linux-x86.ncbi.mk ncbi/ncbi/platform/linux-x86.ncbi.mk
---- ncbi.orig/ncbi/platform/linux-x86.ncbi.mk	2009-02-04 15:24:03.000000000 +0100
-+++ ncbi/ncbi/platform/linux-x86.ncbi.mk	2009-03-27 01:38:18.000000000 +0100
-@@ -11,8 +11,8 @@
- NCBI_AR=ar
- NCBI_CC = gcc -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_GNU_SOURCE
- NCBI_CFLAGS1 = -c
--NCBI_LDFLAGS1 = -O3 -mcpu=pentium4
--NCBI_OPTFLAG = -O3 -mcpu=pentium4
-+NCBI_LDFLAGS1 = -O2 -march=i686 -mtune=i686
-+NCBI_OPTFLAG = -O2 -march=i686 -mtune=i686
- NCBI_BIN_MASTER = /home/coremake/ncbi/bin
- NCBI_BIN_COPY = /home/coremake/ncbi/bin
- NCBI_INCDIR = /home/coremake/ncbi/include

ap/ncbi-toolkit/doinst.sh

@@ -1,12 +0,0 @@
-#!/bin/sh
-config()
-{
-    NEW="$1"
-    OLD="`dirname $NEW`/`basename $NEW .new`"
-    if [ ! -r $OLD ]; then
-        mv $NEW $OLD
-    elif [ "`cat $OLD | md5sum`" = "`cat $NEW | md5sum`" ]; then
-        rm $NEW
-    fi
-}
-config /etc/ncbi/ncbirc.new

ap/ncbi-toolkit/ncbi-toolkit.SlackBuild

@@ -1,143 +0,0 @@
-#!/bin/bash
-# Build script for Slackware
-# Copyright (C) 2008,2009,2010,2011 Damien Goutte-Gattat
-#
-# Redistribution and use of this script, with or without modifications,
-# is permitted provided that the following conditions are met:
-#
-# 1. Redistributions of this script must retain the above copyright
-#    notice, this list of conditions and the following disclaimer.
-#
-# THIS SOFTWARE IS PROVIDED BY THE AUTHOR AS IS'' AND ANY EXPRESS OR
-# IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-# DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT,
-# INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
-# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
-# HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
-# STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
-# IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
-# POSSIBILITY OF SUCH DAMAGE.
-#
-# Contact: Damien Goutte-Gattat <dgouttegattat@incenp.org>
-#
-# Latest ncbi sourcecode is available at:
-# <ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/CURRENT>.
-
-# Source package infos
-NAMESRC=${NAMESRC:-ncbi}
-VERSION=${VERSION:-6.1}
-ARCHIVE=${ARCHIVE:-$NAMESRC.tar.gz}
-WGET=${WGET:-ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/old/20090809/$ARCHIVE}
-
-# Built package infos
-NAMEPKG=${NAMEPKG:-ncbi-toolkit}
-BUILD=${BUILD:-1GGD}
-ARCH=${ARCH:-$(uname -m | sed 's/^i.86$/i486/;s/^arm.*/arm/')}
-EXT=${EXT:-txz}
-
-# Directories
-TMP=${TMP:-/tmp}
-OUT=${OUT:-$TMP/build}
-PKG=${PKG:-$OUT/$NAMEPKG}
-CWD=$(pwd)
-
-set -e  # Quit if a command returns non-zero
-
-# Sanity checks
-if [ $UID -eq 0 ]; then
-    echo "You should NOT run this script as ROOT!"
-    exit 1
-fi
-if [ ! -d $TMP ]; then
-    echo "$TMP does not exist or is not a directory!"
-    exit 1
-fi
-
-# Library directory
-case "$ARCH" in
-x86_64)
-    LIBDIRSUFFIX="64"
-    ;;
-*)
-    LIBDIRSUFFIX=""
-    ;;
-esac
-
-
-# Get and verify the source archive
-if [ ! -r $ARCHIVE ]; then
-    wget -c -O $ARCHIVE.part "$WGET"
-    mv $ARCHIVE.part $ARCHIVE
-fi
-sha1sum -c $ARCHIVE.sha1
-NAME=$(tar ft $ARCHIVE | head -n 1 | cut -d / -f 1)
-
-# Build
-cd $TMP
-echo "Building $ARCHIVE..."
-mkdir ncbi && cd ncbi
-tar xf $CWD/$ARCHIVE
-patch -p 1 < $CWD/build-fixes.diff
-./ncbi/make/makedis.csh
-
-# Install binaries and include files
-mkdir -p $PKG/usr/include
-cp -aL ncbi/bin $PKG/usr/bin
-rm $PKG/usr/bin/{demo*,dosimple,test*}
-mv $PKG/usr/bin/wblast2.REAL $PKG/usr/bin/wblast2
-mv $PKG/usr/bin/wblast2_cs.REAL $PKG/usr/bin/wblast2_cs
-cp -aL ncbi/lib $PKG/usr/lib$LIBDIRSUFFIX
-strip --strip-unneeded $PKG/usr/bin/* $PKG/usr/lib$LIBDIRSUFFIX/*
-cp -aL ncbi/include $PKG/usr/include/ncbi
-rm $PKG/usr/include/ncbi/{cn3d*,pcre*,vib*}
-
-# Install and compress man pages
-mkdir -p $PKG/usr/man
-cp -aL ncbi/doc/man $PKG/usr/man/man1
-rm $PKG/usr/man/man1/{Psequin.1,asnval.1,cleanasn.1,ddv.1,entrez2.1,\
-fmerge.1,gbseqget.1,insdseqget.1,nps2gps.1,sortbyquote.1,spidey.1,\
-trna2sap.1,trna2tbl.1,udv.1}
-find $PKG/usr/man/man1 -type f -exec gzip -9 {} \;
-
-# Install shared NCBI data
-mkdir -p $PKG/usr/share/ncbi
-cp -aL ncbi/data $PKG/usr/share/ncbi
-
-# Install the documentation
-DOCDIR=$PKG/usr/doc/$NAMEPKG-$VERSION
-mkdir -p $DOCDIR
-cp ncbi/README{,.htm} ncbi/VERSION $DOCDIR
-cp ncbi/config/README $DOCDIR/README.config
-cp ncbi/network/nsclilib/readme $DOCDIR/README.net-cfg
-cp -aL ncbi/doc/* $DOCDIR
-rm -rf $DOCDIR/man
-
-# Install the default config file
-install -D -m 644 $CWD/ncbirc $PKG/etc/ncbi/ncbirc.new
-
-# Sanitize permissions
-find $PKG -type d -exec chmod 755 {} \;
-find $PKG -type f -exec chmod 644 {} \;
-find $PKG/usr/bin -type f -exec chmod 755 {} \;
-
-# Copy slack-desc and doinst.sh files
-mkdir -p $PKG/install
-install -m 644 $CWD/slack-desc $PKG/install/slack-desc
-install -m 755 $CWD/doinst.sh  $PKG/install/doinst.sh
-
-# Package the tree
-cd $PKG
-mkdir -p $OUT
-PACKAGING="
-chown root:root . -R
-/sbin/makepkg -l y -c n $OUT/$NAMEPKG-$VERSION-$ARCH-$BUILD.$EXT
-rm -rf $PKG
-rm -rf $TMP/$NAME
-"
-if type -p fakeroot ; then
-    echo "$PACKAGING" | fakeroot
-else
-    su -c "$PACKAGING"
-fi

ap/ncbi-toolkit/ncbi.tar.gz.sha1

@@ -1 +0,0 @@
-9727c13d94cc06cfe2f70148fa6bc5dfe011af50  ncbi.tar.gz

ap/ncbi-toolkit/ncbirc

@@ -1,3 +0,0 @@
-[NCBI]
-DATA=/usr/share/ncbi/data
-

ap/ncbi-toolkit/slack-desc

@@ -1,13 +0,0 @@
-            |-----handy-ruler------------------------------------------------------|
-ncbi-toolkit: ncbi-toolkit (NCBI Software Development Toolkit)
-ncbi-toolkit: 
-ncbi-toolkit: The NCBI Software Development Toolkit has been used for the
-ncbi-toolkit: production and distribution of GenBank, Entrez, BLAST, and related
-ncbi-toolkit: services by NCBI.  It is freely available without restriction to
-ncbi-toolkit: facilitate the use of NCBI by the scientific community.
-ncbi-toolkit: 
-ncbi-toolkit: 
-ncbi-toolkit: 
-ncbi-toolkit: 
-ncbi-toolkit: 
-